Issue 54 | April 2024
Dear reader,

In this edition of the newsletter find out more about recent developments to our key software tools which have been influenced by the feedback provided by users through the surveys we ran during 2023. Registration for our main event of the year is now open: the second BioExcel Conference on Advances in Biomolecular Simulations. If you are interested in joining the GROMACS development team, there is a researcher position available based in Stockholm, Sweden. Our next webinar is scheduled for the end of May and features FAIR workflows in BioExcel Building Blocks (BioBB). We highlight the most excellent podcast series by Miłosz Wieczór called "Phase Space Invaders". Whether you are new to the field or a hardened veteran you are bound to find this interesting! We briefly feature the recent Computational Chemistry Spring School which took place at CSC in Finland and provide access to the materials used.

The BioExcel Team

BioExcel core software updates

We provide a short update on some of the recent work carried out on our key applications. This work is based on the priorities which emerged from our 2023 user surveys and is reflected in our software development dashboard.
GROMACS: The end of February saw the minor release of GROMACS 2024.1 which comes with a number of bug fixes. None of the issues were expected to have caused any errors in the simulation results. To know more on GROMACS 2024 you can watch "GROMACS 2024: new features and improvements" and if you want to know more on the GROMACS-COLVARS interface watch "Enhanced sampling in collective variable space using the Colvars library in GROMACS" on the BioExcel YouTube channel. The developers are working hard to bring requested features into the 2025 release. As always, you are welcome to the user forum if you need help with your simulations.
HADDOCK: March 2024 saw HADDOCK2.X releases of haddock2.4 (Python2.7) and haddock2.5 (python3) containing minor updates regarding the treatment of glycans and additional parameters for D-amino acids.
A fast RMSD calculation C code has been incorporated into HADDOCK3 which enables a very efficient calculation of RMSD matrices for more than 10,000 models, something that was computationally too expensive previously. This is implemented in the rmsdmatrix and ilrmsdmatrix modules. Following a second user requirement, the presentation of results has been improved ("improved analysis results"). The docking runs contain an analysis directory with html files reporting on the cluster statistics and presenting various plots to visualise the results in a similar way to what the HADDOCK server is presenting.
BioExcel Building Blocks (BioBB): BioBB workflows are now also available through Docker containers. Also, see below for our upcoming webinar featuring BioBB.

Second BioExcel Conference: registration open

Registration is open for the second BioExcel Conference on Advances in Biomolecular Simulations which will take place from 20 to 23 October in Brno, Czech Republic.
The conference will gather the biomolecular research community to explore the latest trends, updates and challenges in the fields of integrative modelling, free energy and drug design, workflows, automation and data integration. We have a confirmed list of top speakers from across Europe and the US and are looking to further complement this with additional speakers which will be selected from the submitted abstracts.
More information on registration and abstract submission. Early bird registration closes on the 15th June!

Job opening: Researcher in High Performance Computing (HPC) with GROMACS

We are looking for an HPC expert to contribute to projects related to the GROMACS molecular simulation software. The focus will be on developing new algorithms and co-design motivated by the challenges of new hardware. The position is based in KTH Royal Institute of Technology, Stockholm, Sweden. Find out more about the position and apply
The deadline for applications is 24 May 2024

Webinar: FAIR biomolecular simulation workflows using BioBB

Our next webinar will be on the 28 May and will feature Adam Hospital from IRB Barcelona who will talk about how to create FAIR and reproducible biomolecular simulation workflows using Jupyter Notebooks and Conda environments.
Registration for the webinar will open next week so look out for updates on our website.

Community feature: Phase Space Invaders podcast

As part of our community-building efforts we are providing a platform for those who have relevant and original content to share for the benefit of the broad biomolecular modeling community.
Check out the "Phase Space Invaders" podcasts by Miłosz Wieczór which feature interesting discussions with influential members of the community and aim to highlight upcoming breakthroughs and future perspectives in the field.
If you have been inspired by this and have original content to share or you are thinking of creating some we can help you gain further outreach. Send us a message:

Feature: Comp Chem Spring School 2024

The 12th Spring School took place at CSC in Espoo, Finland, on 17-19 April 2024 and provided a comprehensive, tutorial-style, hands-on, introductory and intermediate-level treatment of the essential methods for molecular modeling and computational chemistry using modern supercomputers.
The school follows a similar program each year and features a foundation in classical molecular dynamics (MD) and electronic structure theory followed by hands-on sessions at three levels of "difficulty". Recently, machine learning (ML) topics have been added to the program.
If you would like to know more about the school we will soon be publishing a more extensive report. For now, we have made the materials available through Zenodo.

Request: please acknowledge BioExcel support

We are passionate about providing high quality support to users of our codes and have done so for many years. We have a small favour to ask those who have received this support and read this message.
Please take a moment to acknowledge the BioExcel Centre of Excellence as part of your dissemination through journals, presentations or other forms of communication. It would mean the world to us! Further, we would be delighted if you could drop us a quick email at to let us know how we have helped you. Thank you for your continued support!
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